*/
#include "catchallcommand.h"
-#include "globaldata.hpp"
//**********************************************************************************************************************
-vector<string> CatchAllCommand::getValidParameters(){
+vector<string> CatchAllCommand::setParameters(){
try {
- string AlignArray[] = {"sabund","shared","label","inputdir","outputdir"};
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+ //can choose shared or sabund not both, so put them in the same chooseOnlyOneGroup
+ CommandParameter pshared("shared", "InputTypes", "", "", "catchallInputs", "catchallInputs", "none",false,false); parameters.push_back(pshared);
+ CommandParameter psabund("sabund", "InputTypes", "", "", "catchallInputs", "catchallInputs", "none",false,false); parameters.push_back(psabund);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
- m->errorOut(e, "CatchAllCommand", "getValidParameters");
+ m->errorOut(e, "CatchAllCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-CatchAllCommand::CatchAllCommand(){
+string CatchAllCommand::getHelpString(){
try {
- //initialize outputTypes
- vector<string> tempOutNames;
- outputTypes["csv"] = tempOutNames;
- outputTypes["summary"] = tempOutNames;
+ string helpString = "";
+ helpString += "The catchall command interfaces mothur with the catchall program written by Linda Woodard, Sean Connolly and John Bunge.\n";
+ helpString += "For more information about catchall refer to http://www.northeastern.edu/catchall/index.html \n";
+ helpString += "The catchall executable must be in the same folder as your mothur executable. \n";
+ helpString += "If you are a MAC or Linux user you must also have installed mono, a link to mono is on the webpage. \n";
+ helpString += "The catchall command parameters are shared, sabund and label. shared or sabund is required. \n";
+ helpString += "The label parameter is used to analyze specific labels in your input.\n";
+ helpString += "The catchall command should be in the following format: \n";
+ helpString += "catchall(sabund=yourSabundFile) \n";
+ helpString += "Example: catchall(sabund=abrecovery.fn.sabund) \n";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "CatchAllCommand", "CatchAllCommand");
+ m->errorOut(e, "CatchAllCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> CatchAllCommand::getRequiredParameters(){
- try {
- string AlignArray[] = {"sabund","shared","or"};
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "CatchAllCommand", "getRequiredParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-vector<string> CatchAllCommand::getRequiredFiles(){
+CatchAllCommand::CatchAllCommand(){
try {
- vector<string> myArray;
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["csv"] = tempOutNames;
+ outputTypes["summary"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "CatchAllCommand", "getRequiredFiles");
+ m->errorOut(e, "CatchAllCommand", "CatchAllCommand");
exit(1);
}
}
/**************************************************************************************/
CatchAllCommand::CatchAllCommand(string option) {
try {
- globaldata = GlobalData::getInstance();
- abort = false;
+
+ abort = false; calledHelp = false;
allLines = 1;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
- //valid paramters for this command
- string Array[] = {"shared","sabund","label","inputdir","outputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
sabundfile = validParameter.validFile(parameters, "sabund", true);
if (sabundfile == "not open") { sabundfile = ""; abort = true; }
else if (sabundfile == "not found") { sabundfile = ""; }
- else { globaldata->setSabundFile(sabundfile); globaldata->setFormat("sabund"); }
+ else { m->setSabundFile(sabundfile); }
sharedfile = validParameter.validFile(parameters, "shared", true);
if (sharedfile == "not open") { sharedfile = ""; abort = true; }
else if (sharedfile == "not found") { sharedfile = ""; }
-
- //check for shared file loaded during read.otu
- if (sharedfile == "") {
- if (globaldata->getSharedFile() != "") { sharedfile = globaldata->getSharedFile(); }
- }
+ else { m->setSharedFile(sharedfile); }
string label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; }
else { allLines = 1; }
}
- if ((sharedfile == "") && (sabundfile == "")) { m->mothurOut("You must provide a sabund or shared file for the catchall command."); m->mothurOutEndLine(); abort=true; }
-
+ if ((sharedfile == "") && (sabundfile == "")) {
+ //is there are current file available for either of these?
+ //give priority to shared, then sabund
+ //if there is a current shared file, use it
+ sharedfile = m->getSharedFile();
+ if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
+ else {
+ sabundfile = m->getSabundFile();
+ if (sabundfile != "") { m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("No valid current files. You must provide a sabund or shared file before you can use the catchall command."); m->mothurOutEndLine();
+ abort = true;
+ }
+ }
+ }
+
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false);
if (outputDir == "not found"){
exit(1);
}
}
-//**********************************************************************************************************************
-
-void CatchAllCommand::help(){
- try {
- m->mothurOut("The catchall command interfaces mothur with the catchall program written by Linda Woodard, Sean Connolly and John Bunge.\n");
- m->mothurOut("For more information about catchall refer to http://www.northeastern.edu/catchall/index.html \n");
- m->mothurOut("The catchall executable must be in the same folder as your mothur executable. \n");
- m->mothurOut("If you are a MAC or Linux user you must also have installed mono, a link to mono is on the webpage. \n");
- m->mothurOut("The catchall command parameters are shared, sabund and label. shared or sabund is required. \n");
- m->mothurOut("The label parameter is used to analyze specific labels in your input.\n");
- m->mothurOut("The catchall command should be in the following format: \n");
- m->mothurOut("catchall(sabund=yourSabundFile) \n");
- m->mothurOut("Example: catchall(sabund=abrecovery.fn.sabund) \n");
- }
- catch(exception& e) {
- m->errorOut(e, "CatchAllCommand", "help");
- exit(1);
- }
-}
-
/**************************************************************************************/
int CatchAllCommand::execute() {
try {
- if (abort == true) { return 0; }
-
- //prepare full output directory
- outputDir = m->getFullPathName(outputDir);
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//get location of catchall
- GlobalData* globaldata = GlobalData::getInstance();
- path = globaldata->argv;
- path = path.substr(0, (path.find_last_of('m')));
+ path = m->argv;
+ path = path.substr(0, (path.find_last_of("othur")-5));
path = m->getFullPathName(path);
-
+
+ savedOutputDir = outputDir;
string catchAllCommandExe = "";
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
catchAllCommandExe += "mono " + path + "CatchAllcmdL.exe ";
+ if (outputDir == "") { outputDir = "./"; } //force full pathname to be created for catchall, this is necessary because if catchall is in the path it will look for input file whereever the exe is and not the cwd.
#else
catchAllCommandExe += "\"" + path + "CatchAllcmdW.exe\"" + " ";
+ if (outputDir == "") { outputDir = ".\\"; } //force full pathname to be created for catchall, this is necessary because if catchall is in the path it will look for input file whereever the exe is and not the cwd.
#endif
+ //prepare full output directory
+ outputDir = m->getFullPathName(outputDir);
+
vector<string> inputFileNames;
- if (sharedfile != "") { inputFileNames = parseSharedFile(sharedfile); globaldata->setFormat("sabund"); }
+ if (sharedfile != "") { inputFileNames = parseSharedFile(sharedfile); }
else { inputFileNames.push_back(sabundfile); }
for (int p = 0; p < inputFileNames.size(); p++) {
//for each label the user selected
while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
-
+
if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
//create catchall input file from mothur's inputfile
string filename = process(sabund, inputFileNames[p]);
string outputPath = m->getPathName(filename);
-
+
//create system command
string catchAllCommand = "";
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
//wrap entire string in ""
catchAllCommand = "\"" + catchAllCommand + "\"";
#endif
- //run catchall
+
+ //run catchall
system(catchAllCommand.c_str());
- remove(filename.c_str());
+ m->mothurRemove(filename);
filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
+ if (savedOutputDir == "") { filename = m->getSimpleName(filename); }
outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out);
- if (m->control_pressed) { out.close(); for (int i = 0; i < outputNames.size(); i++) {remove(outputNames[i].c_str()); } delete input; delete sabund; return 0; }
+ if (m->control_pressed) { out.close(); for (int i = 0; i < outputNames.size(); i++) {m->mothurRemove(outputNames[i]); } delete input; delete sabund; return 0; }
processedLabels.insert(sabund->getLabel());
userLabels.erase(sabund->getLabel());
//create catchall input file from mothur's inputfile
string filename = process(sabund, inputFileNames[p]);
string outputPath = m->getPathName(filename);
-
+
//create system command
string catchAllCommand = "";
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
//run catchall
system(catchAllCommand.c_str());
- remove(filename.c_str());
+ m->mothurRemove(filename);
filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
+ if (savedOutputDir == "") { filename = m->getSimpleName(filename); }
outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out);
- if (m->control_pressed) { out.close(); for (int i = 0; i < outputNames.size(); i++) {remove(outputNames[i].c_str()); } delete input; delete sabund; return 0; }
+ if (m->control_pressed) { out.close(); for (int i = 0; i < outputNames.size(); i++) {m->mothurRemove(outputNames[i]); } delete input; delete sabund; return 0; }
processedLabels.insert(sabund->getLabel());
userLabels.erase(sabund->getLabel());
//run catchall
system(catchAllCommand.c_str());
- remove(filename.c_str());
+ m->mothurRemove(filename);
filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
+ if (savedOutputDir == "") { filename = m->getSimpleName(filename); }
outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
out.close();
delete input;
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {m->mothurRemove(outputNames[i]); } return 0; }
}
if (sharedfile == "") {
- string summaryfilename = outputDir + m->getRootName(m->getSimpleName(inputFileNames[0])) + "catchall.summary";
+ string summaryfilename = savedOutputDir + m->getRootName(m->getSimpleName(inputFileNames[0])) + "catchall.summary";
summaryfilename = m->getFullPathName(summaryfilename);
outputNames.push_back(summaryfilename); outputTypes["summary"].push_back(summaryfilename);
}else { //combine summaries
try {
ofstream out;
- string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "catchall.summary";
+ string combineFileName = savedOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + "catchall.summary";
//open combined file
m->openOutputFile(combineFileName, out);
numLines = thisFilesLines.size();
temp.close();
- remove(outputNames[i].c_str());
+ m->mothurRemove(outputNames[i]);
}
//for each label
//clears file before we start to write to it below
for (int i=0; i<lookup.size(); i++) {
- remove((sharedFileRoot + lookup[i]->getGroup() + ".sabund").c_str());
+ m->mothurRemove((sharedFileRoot + lookup[i]->getGroup() + ".sabund"));
filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".sabund"));
groups.push_back(lookup[i]->getGroup());
}
projects / mothur.git / blobdiff